Sequence
atgc intronic sequence ATGC exonic sequencegtaggctgatactttgatgtgggaatctttataatcttgcaagagtagttatttaagttaaaggctgctgatagtagataaacaatcaatggtaaatattatctttcctaacactttgaaatggatattctcagGCTGCAGTACTAGCTTTGGATGAGTCAGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAG
Basic information
species | Glycine max |
transcript | GLYMA17G11100.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os07g40510.1 (Oryza sativa), 3'ss of exon 3
gtaggctgatactttgatgtgggaatctttataatcttgcaagagtagttatttaagttaaaggctgctgatagtagataaacaatcaatggtaaatattatctttcctaacactttgaaatggatattctcagGCTGCAGTACTAGCTTTGGATGAGTCAGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAG
||| |||| | | || |||| | | |||| || | || || | | || ||| || || | | || ||| | | || |||| | || |||||||||||||||||||| |||||||| ||||| |||||||| ||||| || ||||| ||| | |||
--------------------------------------------gtaattatcttataaaacaagcaaagataatggt--aaca-----tgattgattttttatatcttaatggcttaaattt----tctctagAGTGCGGCTTTGGCACTGGACCAATCTACCTTGGATGTTGATCAAGTGGAGAATCTCATAAAGTTCTGTCCTACAAAAGAAGAAATGGAACTTCTCAAG
upper sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os04g17130.1 (Oryza sativa), 3'ss of exon 8
gtaggctgatactttgatgtgggaatctttataatcttgcaagagtagttatttaagttaaaggctgctgatagtagataaacaatcaatggtaaatattatctttcctaacac-tttgaaatggatattctc----------agGCTGCAGTACTAGCTTTGGATGAGTCAGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAG
|| | ||||| | ||| | | || | | |||| | ||||| ||| | | | | | || | || | ||||| || ||| | |||||||||||||| ||||| | || | ||||||| ||||||||||||| || ||||| || || |||||||||||||| ||| | |||
--------------------------------------------gtggacatttac-tcaaaagttactcccattttttaaatggctaccggtaaggcttaaggtgcttcatccattctatatctactttctctacttgtaacagAGTGCTGCTCTAGCTTTGGATGATTCAGTTCTAGACGCTGATCAACTGGAAAATCTCATAAAATTTTGCCCAACAAAAGAGGAGATGGAACTTCTAAAG
upper sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G414002_T02 (Zea mays), 3'ss of exon 6
gtaggctgatactttgatgtgggaatctttataatcttgcaagagtagttatttaagttaaaggctgctgatagtagataaacaatcaatggtaaatattatctttcctaacactttgaaatggatattctcagGCTGCAGTACTAGCTTTGGATGAGTCAGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAG
||| || || ||| || ||| ||| | || || || ||| || | |||| | || | || | || ||| | ||| ||||| || | | ||| | || |||||||||||||||||||| |||||||| ||||| |||||||| ||||| || ||||| ||| | |||
------------------------------gtaagaatg--aggacagt-atacaagataaggtctcactatttta------taatttctgaca--tattgccatt--tgccaat----gattgatttctccagAGTGCAGCTCTCACGCTAGATCAATCTACCTTGGATGTTGATCAAGTGGAGAATCTCATAAAGTTCTGTCCTACGAAAGAAGAAATGGAACTTCTCAAG
upper sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G07740.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaggctgatactttgatgtgggaatctttataatcttgcaagagtagttatttaagttaaaggctgctgatagtagataaacaatcaatggtaaatattatctttcctaacactttgaaatggatattctcagGCTGCAGTACTAGCTTTGGATGAGTCAGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAG
||| | |||| || || | | | | | || | | | | | || || || || || | | | ||| || || || ||||||||||| || || |||||||||| ||| | |||||||||||| | || ||||| || |||||||| || ||||| ||||||||||| || | |||
------------------------------gtaagttcc----agtacctactttacctgagtgaaagtcatgactggttaccctttcatagtttg-atgataattattcaaatttttctttgcatcgtc-cagGCTGCAGTTCTGGCAATGGATGAGTCTGTACTAGATGTTGATCAAATAGAGAATCTTATAAAGTTTTGCCCAACCAAGGAGGAGATGGAGCTACTTAAG
upper sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv17s0000g06640.t01 (Vitis vinifera), 3'ss of exon 8
gtaggctgatactttgatgtgggaatctttataatcttgcaagagtagttatttaagttaaaggctgctgatagtagataaacaatcaatggtaaatattatctttcctaacactttgaaatggatattctcagGCTGCAGTACTAGCTTTGGATGAGTCAGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAG
|| |||| | || | | | ||| || || | || ||| | | | || || | || || | | || | |||||||||||||||||| ||||| ||||||||||| | || |||||||||||||||||||||||||| ||||| || ||||| |||||||||||||| ||| | |||
---------------------------attgctttcttttttgggtccaactatgatttatagtttgattat--tagtttttt--ttattgttaggcagtagctgttgt---ttactgttgtacatattctcagGCTGCAGTTCTAGCAATGGATGAGTCAATTTTAGATGTTGATCAAGTGGAAAATCTCATAAAGTTCTGCCCTACTAAAGAGGAGATGGAACTTCTTAAG
upper sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S246_71V6.1 (Physcomitrella patens), 3'ss of exon 7
----gtaggctgatactttgatgtgggaatctttataatcttgcaagagt---agttatttaagttaaaggctgctgatagtagataaacaa-tcaatggtaaatattatctttcctaacactttgaaatg------gatattct---cagGCTGCAGTACTAGCTTTGGATGAGTCAGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAG
|| || | || || | | | ||| || || | || | | ||| | | | | ||| ||| | | | || ||| | || | | | ||| | ||||| | || || ||| || ||||||| || ||||||||| |||||||||||||||||||||||||| || || || || |||||||||||| | |||
gtaagtgttctaa-acattagtttt---aacttcattcgctgactaggtttcaaaacattcagccaagatgttgc-aatactcgtttcttggctcggtggctggttttcccaacattgagtcttatgttcgcttcttgatatcgtgtgtagAGTGGAGTTCTTTCTTTGGACCCATCTGTATTGGATACAGATCAAGTGGAAAATCTCATTAAGTTCTGCCCAACGAAGGAGGAGATGGATATGCTGAGA
upper sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ37653 (Selaginella moellendorffii), 3'ss of exon 6
gtaggctgatactttgatgtgggaatctttataatcttgcaagagtagttatttaagttaaaggctgctgatagtagataaacaatcaatggtaaatattatctttcctaacactttgaaatggatattctcagGCTGCAGTACTAGCTTTGGATGAGTCAGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAG
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---------------------------------------------------------------------------------gtaagttgctctctacattatgcaatgtggt--ttttacttgagca--ctcagAAAGCAATACTAGCGTTGGATGGGGCAGTACTGGATGTAGATCAGGTTGATAATCTGATCAAGTTTTGTCCAACAAAGGAGGAGATGGAAACGCTCAAG
upper sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ33545 (Selaginella moellendorffii), 3'ss of exon 6
gtaggctgatactttgatgtgggaatctttataatcttgcaagagtagttatttaagttaaaggctgctgatagtagataaacaatcaatggtaaatattatctttcctaacactttgaaatggatattctcagGCTGCAGTACTAGCTTTGGATGAGTCAGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAG
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-------------------------------------------------------------------------gtaagttg-ctctctacattatgcaatgtggttttt---acttccaa-------ctctcagAAAGCAATACTAGCGTTGGATGGGACGGTACTGGATGTTGATCAGGTTGATAATCTGATCAAGTTTTGTCCAACGAAGGAGGAGATGGAAACGCTCAAG
upper sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ15040 (Selaginella moellendorffii), 3'ss of exon 6
gtaggctgatactttgatgtgggaatctttataatcttgcaagagtagttatttaagttaaaggctgctgatagtagataaacaatcaatggtaaatattatctttcctaacactttgaaatggatattctcagGCTGCAGTACTAGCTTTGGATGAGTCAGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAG
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---------------------------------------------------------------------------------gtaagttgctctctacattatgctatgtggt--ttttacttgagca--ctcagAAAGCAATACTAGCGTTGGATGGGACAGTACTGGATGTAGATCAGGTTGATAATCTGATCAAGTTTTGTCCAACAAAGGAGGAGATGGAAACGCTCAAG
upper sequence: GLYMA17G11100.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ36895 (Selaginella moellendorffii), 3'ss of exon 6
gtaggctgatactttgatgtgggaatctttataatcttgcaagagtagttatttaagttaaaggctgctgatagtagataaacaatcaatggtaaatattatctttcctaacactttgaaatggatattctcagGCTGCAGTACTAGCTTTGGATGAGTCAGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAG
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-------------------------------------------------------------------------gtaagttg-ctctctacattatgcaatgtggttttt---acttccaa-------ccctcagAAAGCAATACTAGCGTTGGATGGGACGGTACTGGATGTTGATCAGGTTGATAATCTGATCAAGTTTTGTCCAACGAAGGAGGAGATGGAAACGCTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaacaatcaatggtaaatattatctttcctaacactttgaaatggatattctcagGCTGCAGTACTAGCTTTGGATGAGTCAGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAG
tcctaac putative branch site (score: 1)
tattctc putative PPT
taaatattatcttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggctgatactttgatgtgggaatctttataatcttgcaagagtagttatttaagttaaaggctgctgatagtagataaacaatcaatggtaaatattatctttcctaacactttgaaatggatattctcagGCTGCAGTACTAGCTTTGGATGAGTCAGTATTGGATGTTGATCAAGTGGAAAATCTCATTAAGTTTTGTCCTACCAAAGAGGAGATGGATCTTTTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG